Isolation and regional localization of a large collection (2,000) of single-copy DNA fragments on human chromosome 3 for mapping and cloning tumor suppressor genes

Summary A collection of 2,000 lambda phage-carrying human single-copy inserts (> 700 bp) were isolated from two chromosome-3 flow-sorted libraries. The single-copy DNA fragments were first sorted into 3p and 3q locations and about 700 3p fragments were regionally mapped using a deletion mapping panel comprised of two humanhamster and two-human-mouse cell hybrids, each containing a chromosome 3 with different deletions in the short arm. The hybrids were extensively mapped with a set of standard 3p markers physically localized or ordered by linkage. The deletion mapping panel divided the short arm into five distinct subregions (A-E). The 3p fragments were distributed on 3p regions as follows: region A, 26%; B, 31%; C, 4%; D, 4% and E, 35%. We screened 300 single-copy DNA fragments from the distal part of 3p (regions A and B) with ten restriction endonucleases for their ability to detect restriction fragment length polymorphisms (RFLPs). Of these fragments 110 (36%) were found to detect useful RFLPs: 35% detected polymorphisms with frequency of heterozygosity of 40% or higher, and 25% with frequency of 30% or higher. All polymorphisms originated from single loci and most of them were of the base pair substitution type. These RFLP markers make it possible to construct a fine linkage map that will span the distal part of chromosome 3p and encompasses the von Hippel-Lindau disease locus. The large number of single-copy fragments (2,000) spaced every 100–150 kb on chromosome 3 will make a significant contribution to mapping and sequencing the entire chromosome 3. The 300 conserved chromosome 3 probes will increase the existing knowledge of man-mouse homologies.     

The effects of adrenal and gonadal steroids and K+-canrenoate on the metabolism of aldosterone by rat liver microsomes

The synthesis of polar aldosterone metabolites by rat liver microsomes at physiological concentrations of aldosterone (21.5 nM), was markedly inhibited by progesterone, testosterone, corticosterone, K+-canrenoate and estradiol-17 beta. In contrast, corticosterone and estradiol-17 beta significantly increased the synthesis of reduced aldosterone metabolites by 8- and 15-fold respectively, the majority of which were 5 alpha-reduced products of aldosterone. In experiments at higher substrate (aldosterone) concentrations (20-200 microM) the synthesis of ring A-reduced aldosterone metabolites by liver microsomes followed Michaelis-Menten kinetics with a Km[app] for aldosterone of 160 microM and Vmax[app] of 12.2 nmoles/mg protein/5 min. In these experiments progesterone, testosterone and K+-canrenoate all competitively inhibited the synthesis of reduced metabolites with inhibition constants (Ki [app]) of 70, 85 and 55 microM respectively; however, corticosterone did not. In contrast, estradiol-17 beta increased the rate of synthesis of reduced products by 40%, lowering the Km[app] to 83 microM.     

Age-related changes in body weight,scrotal size and plasma testosterone levels in buffalo bulls (Bubalus bubalis)

Body weight, testicle size and peripheral testosterone concentrations were measured in 35 water buffalo bulls at 5, 15, 17, 21, 25 and 38 months of age. These parameters were studied in all animals during the same month (October), so the changes due to age were independent of changes in photoperiod and temperature. Body weight increased linearly with age. The testicular size measured in terms of scrotal circumference as related to age, showed a curvilinear increase; the average rate of testicular growth was maximum between 15 and 25 months. Plasma testosterone levels were low between 5 and 21 months. A significant rise in plasma concentration of testosterone was observed at 25 months reaching peak levels at 38 months. The mean age of sexually mature bulls at the time of first ejaculation of semen with motile sperm, was 24.9±0.9 months (n=9). It has been concluded that in the Nili-Ravi buffalo bulls the sexually quiescent period (prepubertal) extends up to 15 months of age and sexual maturation as indicated by the presence of motile sperm in the ejaculate is attained at about 25 months.     

Effects of legumes on soil physical quality in a maize crop

The effect of intercropped legumes and three N fertilizer rates in a continuous maize (Zea mays L.) cropping system on the physical properties of two soils were investigated for three years. The legumes, being a mixture of alfalfa, clover and hairy vetch, had a significant cumulative effect on some physical properties of both soil. The lowest stability and smallest mean weight diameter of soil aggregates were associated with monoculture maize plots. Aggregate size and stability were not affected by N fertilization at any of the rates of 0, 70, and 140 kg ha^-1 in intercropped plots, except that aggregate stability was actually reduced by N fertilization in one soil, the Ste. Rosalie clay. In maize plots in both soils, stability and size of soil aggregates were significantly increased with increased added N. Intercropped legumes significantly decreased dry bulk density and soil penetration resistance. Added N had no measurable influence on these compaction factors. Soil water properties were not significantly affected by either intercropping or N fertilization. Positive effects noted on soil aggregation and other physical properties in intercropped plots are the result of enhanced root activity, or incorporation of legumes as green manure, or both. Improvement of soil structure in maize plots associated with increasing N application was the result of increased maize-root residues.     

Kinetic FP-TDI assay for SNP allele frequency determination

Strategies for identifying genetic risk factors in complex diseases by association studies require the comparison of allele frequencies of numerous SNPs between affected and control populations. Theoretically, hundreds of thousands of SNP markers across the genome will have to be genotyped in these studies. Genotyping SNPs one sample at a time is extremely costly and time consuming. To streamline whole genome association studies, some have proposed to screen SNPs by pooling the DNA samples initially for allele frequency determination and perform individual genotyping only when there is a significant discrepancy in allele frequencies between the affected and control populations. Here we describe a new method for determining the allele frequency of SNPs in pooled DNA samples using a two-color primer extension assay with real-time monitoring of fluorescence polarization (named kinetic FP-TDI assay). By comparing the ratio of the rate of incorporation of the two allele-specific dye-terminators, one can calculate the relative amounts of each allele in the pooled sample. The accuracy of allele frequency determination with pooled samples is within 3.3 +/- 0.8% of that determined by genotyping individual samples that make up the pool.     

Simulations inform design of regional occupancy‐based monitoring for a sparsely distributed,territorial species

Sparsely distributed species attract conservation concern, but insufficient information on population trends challenges conservation and funding prioritization. Occupancy‐based monitoring is attractive for these species, but appropriate sampling design and inference depend on particulars of the study system. We employed spatially explicit simulations to identify minimum levels of sampling effort for a regional occupancy monitoring study design, using white‐headed woodpeckers (Picoides albolvartus), a sparsely distributed, territorial species threatened by habitat decline and degradation, as a case study. We compared the original design with commonly proposed alternatives with varying targets of inference (i.e., species range, space use, or abundance) and spatial extent of sampling. Sampling effort needed to achieve adequate power to observe a long‐term population trend (≥80% chance to observe a 2% yearly decline over 20 years) with the previously used study design consisted of annually monitoring ≥120 transects using a single‐survey approach or ≥90 transects surveyed twice per year using a repeat‐survey approach. Designs that shifted inference toward finer‐resolution trends in abundance and extended the spatial extent of sampling by shortening transects, employing a single‐survey approach to monitoring, and incorporating a panel design (33% of units surveyed per year) improved power and reduced error in estimating abundance trends. In contrast, efforts to monitor coarse‐scale trends in species range or space use with repeat surveys provided extremely limited statistical power. Synthesis and applications. Sampling resolutions that approximate home range size, spatially extensive sampling, and designs that target inference of abundance trends rather than range dynamics are probably best suited and most feasible for broad‐scale occupancy‐based monitoring of sparsely distributed territorial animal species.     

Plant growth-promoting Bacillus sp. strain SDA-4 confers Cd tolerance by physio-biochemical improvements,better nutrient acquisition and diminished Cd uptake in Spinacia oleracea L.

Cadmium (Cd) is highly toxic metal for plant metabolic processes even in low concentration due to its longer half-life and non-biodegradable nature. The current study was designed to assess the bioremediation potential of a Cd-tolerant phytobeneficial bacterial strain Bacillus sp. SDA-4, isolated, characterized and identified from Chakera wastewater reservoir, Faisalabad, Pakistan, together with spinach (as a test plant) under different Cd regimes. Spinach plants were grown with and without Bacillus sp. SDA-4 inoculation in pots filled with 0, 5 or 10 mg kg⁻¹ CdCl₂-spiked soil. Without Bacillus sp. SDA-4 inoculation, spinach plants exhibited reduction in biomass accumulation, antioxidative enzymes and nutrient retention. However, plants inoculated with Bacillus sp. SDA-4 revealed significantly augmented growth, biomass accumulation and efficiency of antioxidative machinery with concomitant reduction in proline and MDA contents under Cd stress. Furthermore, application of Bacillus sp. SDA-4 assisted the Cd-stressed plants to sustain optimal levels of essential nutrients (N, P, K, Ca and Mg). It was inferred that the characterized Cd-tolerant PGPR strain, Bacillus sp. SDA-4 has a potential to reduce Cd uptake and lipid peroxidation which in turn maintained the optimum balance of nutrients and augmented the growth of Cd-stressed spinach. Analysis of bioconcentration factor (BCF) and translocation factor (TF) revealed that Bacillus sp. SDA-4 inoculation with spinach sequestered Cd in rhizospheric zone. Research outcomes are important for understanding morpho-physio-biochemical attributes of spinach-Bacillus sp. SDA-4 synergy which might provide efficient strategies to decrease Cd retention in edible plants and/or bioremediation of Cd polluted soil colloids.     

Overview of Strain Characterization in Relation to Serological and Molecular Detection of Citrus tristeza <i>Closterovirus</i>

Tristeza is a devastating viral disease in all the citrus growing countries throughout the world and has killed millions of citrus trees in severely affected orchards. The citrus species grafted on sour orange rootstock are affected by this disease. Predominantly, the sweet orange, grapefruit and lime trees grafted on sour orange exhibit severe symptoms like quick decline, vein clearing, pin holing, bark scaling and degeneration leading to variable symptoms. Symptomatic expression of Citrus tristeza virus (CTV) in different hosts has been attributed to virus isolates which are from severe to mild. Different serological and molecular assays have been deployed to differentiate the strains of CTV. Citrus tristeza virus is diversified towards its strains on the basis of biological, serological and molecular characterization. Phenotypic expression is due to genetic alteration and different molecular basis have now been adopted for strain differentiation. This review will give a brief idea about the different CTV isolates, their characterization based on nucleic acid and serological assays. Different methods along with salient features for strain characterization has also been reviewed. This review will also open the new aspects towards formulation of management strategies through different detection techniques.